Lab 4

library(tidyverse)

## -- Attaching packages -------------- tidyverse 1.3.0 --

## v ggplot2 3.2.1     v purrr   0.3.3
## v tibble  2.1.3     v dplyr   0.8.3
## v tidyr   1.0.2     v stringr 1.4.0
## v readr   1.3.1     v forcats 0.4.0

## -- Conflicts ----------------- tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()

SNPs<- read.table("23andMe_complete.txt", header = TRUE, sep = "\t")
SNPs$chromosome = ordered(SNPs$chromosome, levels=c(seq(1,22),"X","Y","MT"))

Exercise 1

ggplot(SNPs, aes(SNPs$chromosome, fill=SNPs$chromosome))+
  geom_bar(fill="blue")+
  ggtitle("Genotype Counts per Chromsome")+
  scale_x_discrete("Chromosome")+
  scale_y_continuous("Number of SNPs")

Exercise 2

mycolor<- c("AA"="blue", "AC"="blue", "AG"="blue", "AT"="blue","CC"="blue", "CG"="blue", "CT"="blue", "GG"="blue","GT"="blue", "TT"="blue", "A"="red", "C"="red","G"="red", "T"="red", "D"="green", "DD"="green", "DI"="green", "I"="green", "II"="green", "--"="green")

ggplot(SNPs, aes(SNPs$chromosome, fill=genotype))+
  geom_bar()+
  ggtitle("Genotype Counts per Chromosome")+
  scale_x_discrete("Chromosome")+
  scale_y_continuous("Number of SNPs")+
  scale_fill_manual(values=mycolor)

Exercise 3

Genotype counts per chromosome

Exercise 4

sp<- ggplot(SNPs, aes(SNPs$chromosome, fill=genotype))+
  geom_bar(position="dodge")+
  facet_wrap(~genotype, ncol = 2)+
  ggtitle("Genotype Counts per Chromosome")+
  scale_x_discrete("Chromosome")+
  scale_y_continuous("Number of SNPs")+
  theme(axis.text.x = element_text(angle=90, size=7),
        legend.position = "none")
sp

Exercise 5

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
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##     layout

ggplotly(sp)

Exercise 6

library(DT)
y<- subset(SNPs, chromosome=='Y')
datatable(y)

## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html